Pig NPR-B mRNA was sequenced using polymerase chain reaction primers designed from mouse consensus sequences.
Pig Apelin mRNA was sequenced using polymerase chain reaction primers designed from mouse consensus sequences.
The training sets consisted mainly of endogenous LTR consensuses retrieved from RepBase [15]: 23 HML LTRs, 69 gammaretroviruslike human ERV1 LTRs selected according to [4] from a set of 198 human ERV1 sequences and 138 betaretroviruslike ERV2 mouse consensus sequences.
Next, each mouse consensus sequence was searched for MafB motifs by the MAST program of the MEME suite.
Alignments of ultra-high-depth, stranded RNAseq data to the mouse Repbase consensus sequences reflect a more modest overall strand bias in our hands, most evident in species-specific repeat types as opposed to ancestral repeats in the mouse genome [56.2% strand; data not shown].
To address this point, we predicted the secondary mRNA structures from the rat and mouse SHORT1 consensus sequence.
Putative transcription factor binding sites were identified by scanning the entire mouse genome for consensus sequences using the FIMO tool from the MEME Suite (version 4.6) [ 34] with default parameters, using motif models curated from TRANSFAC (version 11) [ 63], JASPAR [ 64], and UniProbe [ 65].
Similarly, the human and mouse Ins(1,3,4 P3 5/6-kinase/Ins 3,4,5,6) 1-kinase contain the sequence LCRKRGXEVVQLNL (X is M in human and I in mouse), which fits the consensus sequences for a KIM and a MAPK-binding site, but not a D-domain.
Probes have been designed against all annotated transposons - approximately 300 mouse and 500 human TE consensus sequences - in both sense and antisense orientations.
Mouse and human specific TE consensus sequences were obtained from Repbase [ 11, 12] and 100 genes were selected as controls, including oncogenes, tumor suppressors, and housekeeping genes.
Scanning of NOS-2 promoters of human, dog, rat and mouse for this consensus sequence obviously detected all known human κB sites but the incidence of putative sites was extremely high: there are 79 sites that match that consensus sequence in human, 80 in chimpanzee, 71 in mouse, and 85 in rat (data not shown).
